Genomics of Zika Virus

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We are investigating the genomics, phylodynamics, and genotype-phenotype correlations of Zika virus (ZIKV). Our interest is to not only generate next-generation sequence data, but to mine this sequence data to better understand the evolution, pathogenesis, and transmission of ZIKV following the outbreak in Brazil in 2015. To meet these goals, we established collaborations across the globe to obtain clinical samples of infected patients or virus isolates, along with the associated metadata. By integrating the sequence data and the associated metadata, we have established laboratory and bioinformatics-based methods that enable us to investigate scientific questions including: the tropism of ZIKV for dendritic cells and the antiviral response of the cells during infection (Bowen et al. 2017); investigating the phylogenetic diversity of strains obtained by Biodefense and Emerging Infections (BEI) Resources and distributed to virologists (manuscript in preparation); the genetic determinants of ZIKV host adaptation in C6/36 mosquito vs. Vero cells; and the diversity of ZIKV circulating in limited geographic regions, including Barbados, Colombia, and the state of Chiapas, Mexico.